Karia H. Kaukinen

Genomic Signatures Predict Migration and Spawning Failure in Wild Canadian Salmon

High mortality of sockeye salmon in the Fraser River is associated with signals of metabolic and immune stress. Long-term population viability of Fraser River sockeye salmon (Oncorhynchus nerka) is threatened by unusually high levels of mortality as they swim to their spawning areas before they spawn. Functional genomic studies on biopsied gill tissue from tagged wild adults that were tracked through ocean and river environments revealed physiological profiles predictive of successful migration and spawning. We identified a common genomic profile that was correlated with survival in each study. In ocean-tagged fish, a mortality-related genomic signature was associated with a 13.5-fold greater chance of dying en route. In river-tagged fish, the same genomic signature was associated with a 50% increase in mortality before reaching the spawning grounds in one of three stocks tested. At the spawning grounds, the same signature was associated with 3.7-fold greater odds of dying without spawning. Functional analysis raises the possibility that the mortality-related signature reflects a viral infection.

Estimation of Stock Composition and Individual Identification of Sockeye Salmon on a Pacific Rim Basis Using Microsatellite and Major Histocompatibility Complex Variation

Abstract The variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was surveyed for over 48,000 sockeye salmon Oncorhynchus nerka sampled from 299 localities ranging from the Columbia River to Japan. For the microsatellite loci, the number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of stock composition of single-population mixtures. In an analysis of single-population mixtures where the Pacific Rim baseline was used for estimation of stock identification, 80% accuracy for the average population was achieved by employing approximately 80 alleles in the analysis. Increasing the accuracy of estimated stock compositions to 90% for the average population required approximately 400 microsatellite alleles. When all loci were used to estimate stock compositions, estimates were above 80% for all sampling sites or populations, above 90% for the lake of origin, and generally above 95% for the region of origin. Analysis of kn...

Stock Identification of Fraser River Sockeye Salmon Using Microsatellites and Major Histocompatibility Complex Variation

Abstract The utility of DNA-based variation for stock identification was evaluated for Fraser River sockeye salmon Oncorhynchus nerka. For this evaluation, the variation at 14 microsatellite loci and one major histocompatibility complex (MHC) locus was determined from approximately 13,000 fish from 47 populations in the drainage. Genetic differentiation among the populations was observed, the overall F ST value for the 14 microsatellite loci surveyed being 0.054 and that for the MHC locus being 0.215. The variation among regions and populations within regions was approximately 20 times as great as that of the annual variation within populations for the microsatellite loci and 28 times as great for the MHC locus. The power of a microsatellite locus for population-specific identification in simulated mixture samples was positively correlated with the number of observed alleles at the locus. Analysis of simulated mixtures indicated that the mean percentage error of estimated stock compositions was less than ...

Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines

Emerging diseases are impacting animals under high‐density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.

Evaluation and Application of Microsatellite and Major Histocompatibility Complex Variation for Stock Identification of Coho Salmon in British Columbia

Abstract Variation at eight microsatellite loci and two linked exons of a major histocompatibility complex (MHC) locus was surveyed in approximately 21,000 coho salmon Oncorhynchus kisutch sampled from 138 localities ranging from southeast Alaska to the Columbia River, the majority of the sites being in British Columbia. The observed regional population structure enabled evaluation of the utility of using microsatellite and MHC variation for estimating the stock composition of coho salmon in mixed-stock fisheries. Both MHC exons were more effective for stock identification than any of the eight microsatellite loci examined. The two MHC exons combined were nearly as effective, on average, as the eight microsatellite loci combined. Some loci were particularly effective at discriminating stocks from specific regions. Mixed-stock analysis provided accurate estimates of contributions from the threatened Thompson River and upper Skeena River stocks, even when they composed less than 5% of the sampled fish. From...

Transcriptomics of environmental acclimatization and survival in wild adult Pacific sockeye salmon (Oncorhynchus nerka) during spawning migration

Environmental shifts accompanying salmon spawning migrations from ocean feeding grounds to natal freshwater streams can be severe, with the underlying stress often cited as a cause of increased mortality. Here, a salmonid microarray was used to characterize changes in gene expression occurring between ocean and river habitats in gill and liver tissues of wild migrating sockeye salmon (Oncorhynchus nerka Walbaum) returning to spawn in the Fraser River, British Columbia, Canada. Expression profiles indicate that the transcriptome of migrating salmon is strongly affected by shifting abiotic and biotic conditions encountered along migration routes. Conspicuous shifts in gene expression associated with changing salinity, temperature, pathogen exposure and dissolved oxygen indicate that these environmental variables most strongly impact physiology during spawning migrations. Notably, transcriptional changes related to osmoregulation were largely preparatory and occurred well before salmon encountered freshwater. In the river environment, differential expression of genes linked with elevated temperatures indicated that thermal regimes within the Fraser River are approaching tolerance limits for adult salmon. To empirically correlate gene expression with survival, biopsy sampling of gill tissue and transcriptomic profiling were combined with telemetry. Many genes correlated with environmental variables were differentially expressed between premature mortalities and successful migrants. Parametric survival analyses demonstrated a broad‐scale transcriptional regulator, cofactor required for Sp1 transcriptional activation (CRSP), to be significantly predictive of survival. As the environmental characteristics of salmon habitats continue to change, establishing how current environmental conditions influence salmon physiology under natural conditions is critical to conserving this ecologically and economically important fish species.

Toxicity of atrazine and nonylphenol in juvenile rainbow trout (Oncorhynchus mykiss): effects on general health, disease susceptibility and gene expression.

Atrazine (ATZ) and nonylphenol (NP) are commonly identified contaminants in aquatic habitats; however, few studies have considered the impact of these endocrine disrupters on immune function and resistance to disease. This study examined the immunotoxicological effects of ATZ and NP at multiple levels of biological organization. Juvenile rainbow trout (Oncorhynchus mykiss) were exposed to a solvent control (0.00625%, v/v anhydrous ethanol), or sub-lethal concentrations of ATZ (59 μg/L and 555 μg/L) or NP (2.3 μg/L or 18 μg/L) for 4d. At the end of exposure, fish were assessed for a number of physiological endpoints, including a host resistance challenge, and liver gene expression was assessed using a salmonid microarray (cGRASP, 32K version 1). While the low ATZ and low NP treatments had no measurable effects on the physiological endpoints measured, fish exposed to the high ATZ concentration (555 μg/L) exhibited significantly elevated plasma cortisol, a decrease in SSI, and decreased lymphocytes and increased monocytes in peripheral blood, with suppression of early immune system processes apparent at the molecular level. In contrast, fish exposed to the high NP concentration (18 μg/L) showed physiological (e.g. significantly elevated LSI) and gene expression changes (e.g. induction of vitellogenin) consistent with estrogenic effects, as well as decreased lymphocytes in the peripheral blood and more limited alterations in immune system related pathways in the liver transcriptome. Fish exposed to high ATZ or NP concentrations incurred higher mortality than control fish following a disease challenge with Listonella anguillarum, while fish exposed to the lower concentrations were unaffected. Microarray analysis of the liver transcriptome revealed a total of 211 unique, annotated differentially regulated genes (DRGs) following high ATZ exposure and 299 DRGs following high NP exposure. Functional (enrichment) analysis revealed effects on immune system function, metabolism, oxygen homeostasis, cell cycle, DNA damage, and other processes affected by ATZ or NP exposure. Overall, this study provides evidence at multiple levels of biological organization that both ATZ and NP are immunotoxic at sub-lethal concentrations and highlights the potential risk posed by these chemicals to wild fish populations.

Heart and skeletal muscle inflammation (HSMI) disease diagnosed on a British Columbia salmon farm through a longitudinal farm study

Heart and skeletal muscle inflammation (HSMI) is an emerging disease of marine-farmed Atlantic Salmon (Salmo salar), first recognized in 1999 in Norway, and later also reported in Scotland and Chile. We undertook a longitudinal study involving health evaluation over an entire marine production cycle on one salmon farm in British Columbia (Canada). In previous production cycles at this farm site and others in the vicinity, cardiac lesions not linked to a specific infectious agent or disease were identified. Histologic assessments of both live and moribund fish samples collected at the farm during the longitudinal study documented at the population level the development, peak, and recovery phases of HSMI. The fish underwent histopathological evaluation of all tissues, Twort’s Gram staining, immunohistochemistry, and molecular quantification in heart tissue of 44 agents known or suspected to cause disease in salmon. Our analysis showed evidence of HSMI histopathological lesions over an 11-month timespan, with the prevalence of lesions peaking at 80–100% in sampled fish, despite mild clinical signs with no associated elevation in mortalities reported at the farm level. Diffuse mononuclear inflammation and myodegeneration, consistent with HSMI, was the predominant histologic observation in affected heart and skeletal muscle. Infective agent monitoring identified three agents at high prevalence in salmon heart tissue, including Piscine orthoreovirus (PRV), and parasites Paranucleospora theridion and Kudoa thyrsites. However, PRV alone was statistically correlated with the occurrence and severity of histopathological lesions in the heart. Immunohistochemical staining further localized PRV throughout HSMI development, with the virus found mainly within red blood cells in early cases, moving into the cardiomyocytes within or, more often, on the periphery of the inflammatory reaction during the peak disease, and reducing to low or undetectable levels later in the production cycle. This study represents the first longitudinal assessment of HSMI in a salmon farm in British Columbia, providing new insights on the pathogenesis of the disease.

Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka)

The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non‐neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations.

Facing warm temperatures during migration: cardiac mRNA responses of two adult Oncorhynchus nerka populations to warming and swimming challenges.

The main findings of the current study were that exposing adult sockeye salmon Onchorhynchus nerka to a warm temperature that they regularly encounter during their river migration induced a heat shock response at an mRNA level, and this response was exacerbated with forced swimming. Similar to the heat shock response, increased immune defence-related responses were also observed after warm temperature treatment and with a swimming challenge in two different populations (Chilko and Nechako), but with some important differences. Microarray analyses revealed that 347 genes were differentially expressed between the cold (12-13° C) and warm (18-19° C) treated fish, with stress response (GO:0006950) and response to fungus (GO:0009620) elevated with warm treatment, while expression for genes involved in oxidative phosphorylation (GO:0006119) and electron transport chain (GO:0022900) elevated for cold-treated fish. Analysis of single genes with real-time quantitative PCR revealed that temperature had the most significant effect on mRNA expression levels, with swimming and population having secondary influences. Warm temperature treatment for the Chilko population induced expression of heat shock protein (hsp) 90α, hsp90β and hsp30 as well as interferon-inducible protein. The Nechako population, which is known to have a narrower thermal tolerance window than the Chilko population, showed even more pronounced stress responses to the warm treatment and there was significant interaction between population and temperature treatment for hsp90β expression. Moreover, significant interactions were noted between temperature treatment and swimming challenge for hsp90α and hsp30, and while swimming challenge alone increased expression of these hsps, the expression levels were significantly elevated in warm-treated fish swum to exhaustion. In conclusion, it seems that adult O. nerka currently encounter conditions that induce several cellular defence mechanisms during their once-in-the-lifetime migration. As river temperatures continue to increase, it remains to be seen whether or not these cellular defences provide sufficient protection for all O. nerka populations.